Computational Biology Tools
Genomation
Genomation is a Bioc R package that provides collection og functions for simplfiying common tasks in genomic feature/interval analysis. It provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. It can also annotate given regions with other genomic features such as exons,introns and promoters.
People: Altuna Akaling and Vedran Franke and others
GitHub: https://github.com/BIMSBbioinfo/genomation
MethylKit
methylKit is a Bioc R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods such as Agilent SureSelect methyl-seq. In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.
People: Altuna Akalin and Alex Blume and others
GitHub: https://github.com/al2na/methylKit
MotifActivity
The motifActivity R package predicts key transcription factors (TFs) driving gene expression or epigenetic marks changes across the input samples, and the activity profiles of TFs. As input is uses a set of gene expression (e.g. RNA-seq) or epigenetic marks (such as from BS-seq, ChIP-seq, ATAC-seq etc.) across samples, and a set of DNA motifs.
People: Katarzyna Wreczycka
GitHub: https://github.com/katwre/motifActivity
Customized enhancements and additional functionalities for existing tool
IGV web application
Enhancements of an interactive tool for the visual exploration of genomic data called IGV web application included: - visualization of publicly-available and in-house data and dynamic adding new in-house data to the IGV application - added and highlight regions of interest, such as genetic variants to the main window - new visualization options for RefSeq and GENCODE gene annotations: collapse all genes transcripts, extend isoforms of a gene of interest, and added a button to control the width of window panes so that the contents fit - added display links to databases from which data originates - implemented a command line application that automatically takes snapshots and session of regions/genes and tracks of interest
